Fitting Linear Mixed-Effects Models Using lme4
TLDR
In this article, a model is described in an lmer call by a formula, in this case including both fixed-and random-effects terms, and the formula and data together determine a numerical representation of the model from which the profiled deviance or the profeatured REML criterion can be evaluated as a function of some of model parameters.Abstract:
Maximum likelihood or restricted maximum likelihood (REML) estimates of the parameters in linear mixed-effects models can be determined using the lmer function in the lme4 package for R. As for most model-fitting functions in R, the model is described in an lmer call by a formula, in this case including both fixed- and random-effects terms. The formula and data together determine a numerical representation of the model from which the profiled deviance or the profiled REML criterion can be evaluated as a function of some of the model parameters. The appropriate criterion is optimized, using one of the constrained optimization functions in R, to provide the parameter estimates. We describe the structure of the model, the steps in evaluating the profiled deviance or REML criterion, and the structure of classes or types that represents such a model. Sufficient detail is included to allow specialization of these structures by users who wish to write functions to fit specialized linear mixed models, such as models incorporating pedigrees or smoothing splines, that are not easily expressible in the formula language used by lmer.read more
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Evolutionary pressure against MHC class II binding cancer mutations
Rachel Marty Pyke,Wesley K. Thompson,Rany M. Salem,Joan Font-Burgada,Joan Font-Burgada,Maurizio Zanetti,Hannah Carter +6 more
TL;DR: It is demonstrated that the M HC-II genotype constrains the mutational landscape during tumorigenesis in a manner complementary to MHC-I, emphasizing the central role of MHC -II presentation in tumor evolution.
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Depressive symptoms, mental wellbeing, and substance use among adolescents before and during the COVID-19 pandemic in Iceland: a longitudinal, population-based study.
Ingibjorg E. Thorisdottir,Bryndis Bjork Asgeirsdottir,Alfgeir L. Kristjansson,Alfgeir L. Kristjansson,Heiddis B. Valdimarsdottir,Heiddis B. Valdimarsdottir,Erla Maria Jonsdottir Tolgyes,Jon Sigfusson,John P. Allegrante,Inga Dora Sigfusdottir,Inga Dora Sigfusdottir,Thorhildur Halldorsdottir,Thorhildur Halldorsdottir +12 more
TL;DR: In this article, the authors investigated the effect of the COVID-19 pandemic on mental health and substance use during this sensitive developmental stage and found that the decrease observed in substance use might be an unintended benefit of isolation, and might serve as a protective factor against future substance use disorders and dependence.
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Corn yield response to winter cover crops: An updated meta-analysis
G.S. Marcillo,Fernando E. Miguez +1 more
TL;DR: The results suggest that benefits of WCCs do not result in reduced corn productivity if properly managed, and evidence of 65 years of research showed that uncertainty around the RR has decreased and corn yield response to W CCs has stabilized over time.
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DNA methylation analysis on purified neurons and glia dissects age and Alzheimer's disease-specific changes in the human cortex
Gilles Gasparoni,Sebastian Bultmann,Pavlo Lutsik,Theo F. J. Kraus,Sabrina Sordon,Julia Vlcek,Vanessa Dietinger,Martina Steinmaurer,Melanie Haider,Christopher B. Mulholland,Thomas Arzberger,Sigrun Roeber,Matthias Riemenschneider,Hans A. Kretzschmar,Armin Giese,Heinrich Leonhardt,Jörn Walter +16 more
TL;DR: This first EWAS based on sorted neuronal and non-neuronal nuclei from postmortem human brain tissues shows that cell sorting strongly enhances the robust detection of disease-related DNA methylation changes even in a relatively small cohort and reveals two novel previously unrecognizedmethylation changes at the key AD risk genes APP and ADAM17.
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Consolidation Promotes the Emergence of Representational Overlap in the Hippocampus and Medial Prefrontal Cortex.
TL;DR: It is found that neural patterns in the hippocampus and medial prefrontal cortex represented the featural overlap across memories, but only after a week, suggesting a trade-off between the integration of related memories and recovery of episodic details.
References
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